Input and runtime details for job 5882223 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation	Additional homologs
185	0.008247	0.1556	b4195	ulaC	-8.57	0.111851	181 -- 191	40 -- 50	L-ascorbate-specific enzyme IIA component of PTS		_____________180_________192\n_____________\|___________\|\n5'-GCG...GCAGG___________GGACG...UGG-3'\n______________AUGUGAAGUAA\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UGCACUUCAUU\n3'-AUU...GCUAA___________UUCCA...AUG-5'\n_____________\|___________\|\n_____________51__________39\n	185 -- 191	40 -- 46	-13.163 kcal/mol	1.2893 kcal/mol	3.32158 kcal/mol	180 192@LB@ \| \|@LB@5'-GCG...GCAGG GGACG...UGG-3'@LB@ AUGUGAAGUAA@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UGCACUUCAUU@LB@3'-AUU...GCUAA UUCCA...AUG-5'@LB@ \| \|@LB@ 51 39@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -13.163 kcal/mol@LB@Unfolding Energy - mRNA 1.2893 kcal/mol@LB@Unfolding Energy - sRNA 3.32158 kcal/mol@LB@@LB@Position - mRNA 181 -- 191@LB@Position - sRNA 40 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 40 -- 46@LB@
99	0.00311	0.1096	b2801	fucP	-13.12	0.004165	162 -- 172	46 -- 56	L-fucose transporter		_____________161_________173\n_____________\|___________\|\n5'-AUG...CAUAA___________CUUAA...CAC-3'\n______________CCGAUUACGUG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCAC\n3'-AUU...GUUUA___________UUCAU...AUG-5'\n_____________\|___________\|\n_____________57__________45\n	166 -- 172	46 -- 52	-17.4041 kcal/mol	2.44124 kcal/mol	1.86194 kcal/mol	161 173@LB@ \| \|@LB@5'-AUG...CAUAA CUUAA...CAC-3'@LB@ CCGAUUACGUG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCAC@LB@3'-AUU...GUUUA UUCAU...AUG-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -17.4041 kcal/mol@LB@Unfolding Energy - mRNA 2.44124 kcal/mol@LB@Unfolding Energy - sRNA 1.86194 kcal/mol@LB@@LB@Position - mRNA 162 -- 172@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 46 -- 52@LB@
8	1.842e-05	0.007771	b2797	sdaB	-15.07	0.000654	133 -- 147	55 -- 69	L-serine dehydratase 2		_____________132_____________148\n_____________\|_______________\|\n5'-CGA...CUCUC_______________UUUCG...UGA-3'\n______________UGUUCAGCUAAGUCC\n______________\|:\|\|\|\|\|\|:\|\|:\|\|\|\n______________AUAAGUCGGUUUAGG\n3'-AUU...AUUUU_______________CUAAU...AUG-5'\n_____________\|_______________\|\n_____________70______________54\n	141 -- 147	55 -- 61	-22.3059 kcal/mol	1.18067 kcal/mol	6.0797 kcal/mol	132 148@LB@ \| \|@LB@5'-CGA...CUCUC UUUCG...UGA-3'@LB@ UGUUCAGCUAAGUCC@LB@ \|:\|\|\|\|\|\|:\|\|:\|\|\|@LB@ AUAAGUCGGUUUAGG@LB@3'-AUU...AUUUU CUAAU...AUG-5'@LB@ \| \|@LB@ 70 54@LB@@LB@@LB@Energy -15.07 kcal/mol@LB@Hybridization Energy -22.3059 kcal/mol@LB@Unfolding Energy - mRNA 1.18067 kcal/mol@LB@Unfolding Energy - sRNA 6.0797 kcal/mol@LB@@LB@Position - mRNA 133 -- 147@LB@Position - sRNA 55 -- 69@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 55 -- 61@LB@
25	0.0002052	0.02687	b0885	aat	-14.70	0.000956	173 -- 191	42 -- 59	leucyl/phenylalanyl-tRNA-protein transferase		_____________172_________________192\n_____________\|___________________\|\n5'-CGU...UGAAC_______C___________UUUGC...UUA-3'\n______________GAUCCGA_UUGCGUGGAGU\n______________:\|\|\|\|\|\|_\|\|:\|\|\|\|:\|\|\|\n______________UUAGGCU_AAUGCACUUCA\n3'-AUU...UCGGU___________________UUUUC...AUG-5'\n_____________\|___________________\|\n_____________60__________________41\n	185 -- 191	42 -- 48	-23.9715 kcal/mol	6.00825 kcal/mol	3.27976 kcal/mol	172 192@LB@ \| \|@LB@5'-CGU...UGAAC C UUUGC...UUA-3'@LB@ GAUCCGA UUGCGUGGAGU@LB@ :\|\|\|\|\|\| \|\|:\|\|\|\|:\|\|\|@LB@ UUAGGCU AAUGCACUUCA@LB@3'-AUU...UCGGU UUUUC...AUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -23.9715 kcal/mol@LB@Unfolding Energy - mRNA 6.00825 kcal/mol@LB@Unfolding Energy - sRNA 3.27976 kcal/mol@LB@@LB@Position - mRNA 173 -- 191@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 42 -- 48@LB@
44	0.000471	0.03766	b3624	waaZ	-7.10	0.250129	289 -- 295	1 -- 7	lipopolysaccharide KdoIII transferase; lipopolysaccharide core biosynthesis protein		_____________288_____296\n_____________\|_______\|\n5'-AGA...UUCGG_______AUCGC-3'\n______________GCCCUAC\n______________:\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	289 -- 295	1 -- 7	-11.6335 kcal/mol	2.52016 kcal/mol	2.03949 kcal/mol	288 296@LB@ \| \|@LB@5'-AGA...UUCGG AUCGC-3'@LB@ GCCCUAC@LB@ :\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -11.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.52016 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 1 -- 7@LB@
21	0.0001601	0.02641	b2344	fadL	-13.31	0.003531	80 -- 135	1 -- 58	long-chain fatty acid outer membrane transporter		_____________79_________________________________________________________________136\n_____________\|__________________________________________________________________\|\n5'-UCC...AGCUG______CCUA___UCUCGCCACU________UUUCU____________________A_________ACUUC...UUU-3'\n______________GUCCGA____UAC___________GGUCUGA_____AAGAUG________UACCUC_G_ACCCUAC\n______________:\|\|\|\|\|____\|\|\|___________\|\|\|\|\|\|\|_____\|\|\|\|\|:________\|\|\|\|\|\|_\|_\|\|\|\|\|\|\|\n______________UAGGCU____AUG___________CCAGACU_____UUCUAU________AUGGAG_C_UGGGAUG\n3'-AUU...CGGUU______A______CACUUCAUUUU__________________CUUGUAGA______A_A_______-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	129 -- 135	1 -- 7	-38.7471 kcal/mol	12.7593 kcal/mol	12.7027 kcal/mol	79 136@LB@ \| \|@LB@5'-UCC...AGCUG CCUA UCUCGCCACU UUUCU A ACUUC...UUU-3'@LB@ GUCCGA UAC GGUCUGA AAGAUG UACCUC G ACCCUAC@LB@ :\|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|\| \| \|\|\|\|\|\|\|@LB@ UAGGCU AUG CCAGACU UUCUAU AUGGAG C UGGGAUG@LB@3'-AUU...CGGUU A CACUUCAUUUU CUUGUAGA A A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -38.7471 kcal/mol@LB@Unfolding Energy - mRNA 12.7593 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 80 -- 135@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 1 -- 7@LB@
79	0.001698	0.07533	b2890	lysS	-8.16	0.142186	53 -- 64	54 -- 65	lysine tRNA synthetase constitutive	b4129	_____________52___________65\n_____________\|____________\|\n5'-AAA...UGGGG____________UUCUU...GGA-3'\n______________CAGCCAGAUUCG\n______________\|\|\|\|\|\|:\|\|:\|\|\n______________GUCGGUUUAGGC\n3'-AUU...UAUAA____________UAAUG...AUG-5'\n_____________\|____________\|\n_____________66___________53\n	58 -- 64	54 -- 60	-18.439 kcal/mol	4.14677 kcal/mol	6.15795 kcal/mol	52 65@LB@ \| \|@LB@5'-AAA...UGGGG UUCUU...GGA-3'@LB@ CAGCCAGAUUCG@LB@ \|\|\|\|\|\|:\|\|:\|\|@LB@ GUCGGUUUAGGC@LB@3'-AUU...UAUAA UAAUG...AUG-5'@LB@ \| \|@LB@ 66 53@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -18.439 kcal/mol@LB@Unfolding Energy - mRNA 4.14677 kcal/mol@LB@Unfolding Energy - sRNA 6.15795 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 54 -- 65@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 54 -- 60@LB@
159	0.006413	0.1413	b4242	mgtA	-7.15	0.243258	247 -- 262	45 -- 58	magnesium transporter		_____________246______________263\n_____________\|________________\|\n5'-GGU...UUCCC________CAU_____UCCAU...UGG-3'\n______________GUCUGGUU___CGUGA\n______________:\|\|:\|:\|\|___\|\|\|\|\|\n______________UAGGCUAA___GCACU\n3'-AUU...CGGUU________U_______UCAUU...AUG-5'\n_____________\|________________\|\n_____________59_______________44\n	248 -- 254	51 -- 57	-12.639 kcal/mol	3.2244 kcal/mol	2.28003 kcal/mol	246 263@LB@ \| \|@LB@5'-GGU...UUCCC CAU UCCAU...UGG-3'@LB@ GUCUGGUU CGUGA@LB@ :\|\|:\|:\|\| \|\|\|\|\|@LB@ UAGGCUAA GCACU@LB@3'-AUU...CGGUU U UCAUU...AUG-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -12.639 kcal/mol@LB@Unfolding Energy - mRNA 3.2244 kcal/mol@LB@Unfolding Energy - sRNA 2.28003 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 51 -- 57@LB@
102	0.003218	0.1101	b3816	corA	-9.85	0.049984	130 -- 160	4 -- 37	magnesium/nickel/cobalt transporter		_____________129_________________________________161\n_____________\|___________________________________\|\n5'-ACC...UUAAU_________CCCA________GUU___G_______ACCGA...AAC-3'\n______________GGUCUGAAA________AUUU___UCU_UGUGCCC\n______________\|\|\|\|\|\|\|\|\|________\|\|:\|___:\|\|_\|\|\|:\|\|\|\n______________CCAGACUUU________UAGA___GGA_ACAUGGG\n3'-AUU...AUUUU_________CUAUCUUG____AU____G_______AUG-5'\n_____________\|___________________________________\|\n_____________38__________________________________3\n	154 -- 160	4 -- 10	-28.4013 kcal/mol	7.22925 kcal/mol	11.3428 kcal/mol	129 161@LB@ \| \|@LB@5'-ACC...UUAAU CCCA GUU G ACCGA...AAC-3'@LB@ GGUCUGAAA AUUU UCU UGUGCCC@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| :\|\| \|\|\|:\|\|\|@LB@ CCAGACUUU UAGA GGA ACAUGGG@LB@3'-AUU...AUUUU CUAUCUUG AU G AUG-5'@LB@ \| \|@LB@ 38 3@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -28.4013 kcal/mol@LB@Unfolding Energy - mRNA 7.22925 kcal/mol@LB@Unfolding Energy - sRNA 11.3428 kcal/mol@LB@@LB@Position - mRNA 130 -- 160@LB@Position - sRNA 4 -- 37@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 4 -- 10@LB@
126	0.00422	0.1178	b1621	malX	-14.96	0.000732	43 -- 87	1 -- 56	maltose and glucose-specific PTS enzyme IIB component and IIC component		_____________42__________________________________________________________88\n_____________\|___________________________________________________________\|\n5'-AUG...ACUCC____________C___________________A______________UAUU________ACCCG...GCA-3'\n______________CUGAUUAUGUGA_______________AGAUA_AACGUUUUACCUUU____UAUCUUAU\n______________\|:\|\|\|\|\|:\|\|\|\|_______________\|\|\|\|\|_\|\|\|:\|:\|\|\|\|\|\|:\|____\|\|:\|:\|\|:\n______________GGCUAAUGCACU_______________UCUAU_UUGUAGAAUGGAGA____AUGGGAUG\n3'-AUU...GUUUA____________UCAUUUUCCAGACUU_____C______________C___________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	81 -- 87	1 -- 7	-37.7188 kcal/mol	10.08 kcal/mol	12.7022 kcal/mol	42 88@LB@ \| \|@LB@5'-AUG...ACUCC C A UAUU ACCCG...GCA-3'@LB@ CUGAUUAUGUGA AGAUA AACGUUUUACCUUU UAUCUUAU@LB@ \|:\|\|\|\|\|:\|\|\|\| \|\|\|\|\| \|\|\|:\|:\|\|\|\|\|\|:\| \|\|:\|:\|\|:@LB@ GGCUAAUGCACU UCUAU UUGUAGAAUGGAGA AUGGGAUG@LB@3'-AUU...GUUUA UCAUUUUCCAGACUU C C -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -14.96 kcal/mol@LB@Hybridization Energy -37.7188 kcal/mol@LB@Unfolding Energy - mRNA 10.08 kcal/mol@LB@Unfolding Energy - sRNA 12.7022 kcal/mol@LB@@LB@Position - mRNA 43 -- 87@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 1 -- 7@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching